1TAH

THE CRYSTAL STRUCTURE OF TRIACYLGLYCEROL LIPASE FROM PSEUDOMONAS GLUMAE REVEALS A PARTIALLY REDUNDANT CATALYTIC ASPARTATE

• PDB DOI: https://doi.org/10.2210/pdb1TAH/pdb

• Classification: HYDROLASE(CARBOXYLIC ESTERASE)
• Organism(s): Burkholderia glumae
• Mutation(s): No 


• Deposited: 1993-12-21 Released: 1994-05-31 
• Deposition Author(s): Noble, M.E.M., Cleasby, A., Johnson, L.N., Egmond, M., Frenken, L.G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 

Literature

The crystal structure of triacylglycerol lipase from Pseudomonas glumae reveals a partially redundant catalytic aspartate.

Noble, M.E., Cleasby, A., Johnson, L.N., Egmond, M.R., Frenken, L.G.

(1993) FEBS Lett 331: 123-128

• PubMed: 8405390 
• DOI: https://doi.org/10.1016/0014-5793(93)80310-q
• Primary Citation of Related Structures:  
  1TAH


• PubMed Abstract: 
  

  The family of lipases (triacylglycerol-acyl-hydrolases EC 3.1.1.3) constitutes an interesting class of enzymes because of their ability to interact with lipid-water interfaces, their wide range of substrate specificities, and their potential industrial applications. Here we report the first crystal structure of a bacterial lipase, from Pseudomonas glumae. The structure is formed from three domains, the largest of which contains a subset of the alpha/beta hydrolase fold and a calcium site. Asp263, the acidic residue in the catalytic triad, has previously been mutated into an alanine with only a modest reduction in activity.

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Organizational Affiliation: 

Laboratory of Molecular Biophysics, Department of Biochemistry, Oxford, UK.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 132.35 kDa 
• Atom Count: 9,320 
• Modelled Residue Count: 1,272 
• Deposited Residue Count: 1,272 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
LIPASE	A [auth B], B [auth A], C, D	318	Burkholderia glumae	Mutation(s): 0  EC: 3.1.1.3
UniProt
Find proteins for P0DUB8 (Burkholderia plantarii) Explore P0DUB8  Go to UniProtKB:  P0DUB8

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	E [auth B], F [auth A], G [auth C], H [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.00 Å
• R-Value Free: 0.226 
• R-Value Work: 0.159 
• R-Value Observed: 0.159 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 158.16	α = 90
b = 158.64	β = 90
c = 63.36	γ = 90

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 1994-05-31 
Deposition Author(s): Noble, M.E.M., Cleasby, A., Johnson, L.N., Egmond, M., Frenken, L.G.J.

Revision History  

• Version 1.0: 1994-05-31
  Type: Initial release
  
• Version 1.1: 2008-03-03
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-11-29
  Changes: Derived calculations, Other
• Version 1.4: 2024-11-20
  Changes: Data collection, Database references, Derived calculations, Structure summary